I've never had this problem -- In fact it's one of the things I love about this program. "The Other Program" we have here does that all the time. That's why most of our developers like PL/SQL Developer.
Presently I do not think there is an option for this. In the future, I think it would be nice to have an intermediary window between a DDL drag/drop to ask if you want everything, or just table structure.